Decoding from brain imaging data of individual subjects by using additional imaging data from other subjects

ABSTRACT

A computer-implemented method for decoding brain imaging data of individual subjects by using additional imaging data from other subjects includes receiving a plurality of functional Magnetic Resonance Imaging (fMRI) datasets corresponding to a plurality of subjects. Each fMRI dataset corresponds to a distinct subject and comprises brain activation patterns resulting from presentation of a plurality of stimuli to the distinct subject. A group dimensionality reduction (GDR) technique is applied to the example fMRI datasets to yield a low-dimensional space of response variables shared by the plurality of subjects. A model is trained to predict a set of target variables based on the low-dimensional space of response variables shared by all subjects, wherein the set of target variables comprise one or more characteristics of the plurality of stimuli.

GOVERNMENT INTERESTS

This invention was made with government support under grantFA8650-14-C-7358 awarded by Air Force Research Laboratory. Thegovernment has certain rights in the invention.

This research is based upon work supported in part by the Office of theDirector of National Intelligence (ODNI), Intelligence Advanced ResearchProjects Activity (IARPA), via Air Force Research Laboratory (AFRL). Theviews and conclusions contained herein are those of the authors andshould not be interpreted as necessarily representing the officialpolicies or endorsements, either expressed or implied, of ODNI, IARPA,AFRL, or the U.S. Government. The U.S. Government is authorized toreproduce and distribute reprints for Governmental purposesnotwithstanding any copyright annotation thereon.

TECHNICAL FIELD

The present invention relates generally to methods, systems, andapparatuses for improving decoding from brain imaging data of individualsubjects by using additional imaging data from other subjects. Thetechnology described herein may be applied, for example, to answeringclinical questions based on magnetic resonance imaging data.

BACKGROUND

State-of-the-art functional MRI (fMRI) experiments often use complexstimuli, with the ultimate goal being to identify what in the brainactivation encodes characteristics of those stimuli (e.g., visual,semantic, etc.). This is often done by learning a mapping thatassociates the presence of each characteristic with its effect on thepattern of brain activation across voxels. This is then used to decodethose features from new brain imaging data. The mapping is learned withdata for a single subject, and works only on that subject. Any generalconclusion about stimulus representations can only be drawn bycomparing, post-hoc, the brain regions associated with eachcharacteristic, across subjects. Furthermore, functional MRI data arevery noisy, so it may be difficult to learn the mapping for certainsubjects.

Conventional approaches rely on there being multiple subjects on whomcorresponding fMRI datasets—using the same stimuli—were acquired. Forexample, one conventional technique averages data from multiplesubjects. This requires first aligning subjects based on theiranatomical scans—with any registration technique—and then applying thesame transformation to functional imaging data, averaging the resultingtransformed data across subjects. This reduces noise but destroys anyfMRI activation that is not focal and does not overlap across people.This is an issue because it is already known that information resides inthe overall distributed pattern of brain activation, rather than just inspecific locations. A second conventional technique combines data frommultiple subjects into a single representation using a groupdimensionality reduction method. This is effective but means that allsubjects must be available for use at both the time we learn the mappinglearning and the time we use it for testing; any results obtainedpertain to the group, rather than individual subjects.

SUMMARY

Embodiments of the present invention address and overcome one or more ofthe above shortcomings and drawbacks by providing methods, systems, andapparatuses related to improving decoding from brain imaging data ofindividual subjects by using additional imaging data from othersubjects.

According to some embodiments, a computer-implemented method fordecoding from brain imaging data of individual subjects by usingadditional imaging data from other subjects includes receiving aplurality of functional Magnetic Resonance Imaging (fMRI) datasetscorresponding to a plurality of subjects. Each fMRI dataset correspondsto a distinct subject and comprises patterns brain activation resultingfrom presentation of a plurality of stimuli to the distinct subject. Agroup dimensionality reduction (GDR) technique is applied to the examplefMRI datasets to yield a low-dimensional space of response variablesshared by the plurality of subjects. A model (e.g., a Recurrent NeuralNetwork) is trained to predict a set of target variables based on thelow-dimensional space of response variables shared by all subjects. Theset of target variables comprise one or more characteristics of theplurality of stimuli. Once the model is trained, it can be applied tonew fMRI datasets corresponding to new patients by first applying theGDR technique to transform the new fMRI dataset into the low-dimensionalspace and then applying the model to predict one target variable.

Various enhancements, refinements, and other modifications may be madeto the aforementioned method in different embodiments. For example, theGDR technique used in the aforementioned method may be Shared ResponseModelling, Canonical Correlation Analysis, or a supervised SharedResponse Modelling technique that combines application of the GDRtechnique to the example fMRI datasets and training of the model. Thecharacteristics in the target variables may include, for example, avisual representation of one or more stimulus included in the pluralityof stimuli or a semantic representation of one or more stimulus includedin the plurality of stimuli. In some embodiments, at least a portion ofthe plurality of fMRI datasets comprise synthetic datasets. In theseembodiments, the synthetic datasets may be generated using a GenerativeAdversarial Network (GAN) framework comprising a generator, adiscriminator, and a semantic decoder network, wherein the generatorevolves with gradients back-propagated from the semantic decoder networkand the discriminator. In other embodiments, the synthetic datasets aregenerated using a GAN framework comprising a generator and adiscriminator connected using a cyclic consistency constraint thatminimizes the difference between the plurality of stimuli and generatedstimuli produced by the generator.

According to another aspect of the present invention, as described insome embodiments, a second computer-implemented method for decoding frombrain imaging data of individual subjects by using additional imagingdata from other subjects includes receiving a first set of fMRI datasetscorresponding to a plurality of subjects, wherein (a) each fMRI datasetcorresponds to a distinct subject; (b) each fMRI dataset comprisespatterns brain activation resulting from presentation of a plurality ofstimuli to the distinct subject, (c) each fMRI data is in voxel space. AGDR technique is applied to the first set of fMRI datasets to yield alow-dimensional space of response variables shared by the plurality ofsubjects. A second set of fMRI datasets corresponding to the pluralityof subjects is generated by projecting the low-dimensional space ofresponse variables back to voxel space. Then a model is trained topredict a set of target variables based on the second set of fMRIdatasets, wherein the set of target variables comprise one or morecharacteristics of the plurality of stimuli. To apply this model to anew fMRI dataset corresponding to a new subject, the GDR technique isfirst applied to transform the new fMRI dataset into new responsevariables in the low-dimensional space. Next, the low-dimensional spaceof response variables are projected back to voxel space; and the modelto predict one or more target variables. The various features andenhancements discussed above with respect to the first method may besimilarly applied to this second method for decoding from brain imagingdata.

In other embodiments, a system for decoding from brain imaging data ofindividual subjects by using additional imaging data from other subjectsan fMRI scanner and one or more processors. The fMRI scanner isconfigured to acquire an fMRI dataset corresponding to a subject. ThisfMRI dataset comprises brain activation patterns resulting frompresentation of a plurality of stimuli to the distinct subject. Theprocessors are configured to apply a group dimensionality reduction(GDR) technique to the fMRI dataset to transform it into alow-dimensional space of response variables shared by a plurality ofsubjects. The processors apply a machine learning model to thetransformed fMRI dataset to predict one or more target variables.

Additional features and advantages of the invention will be madeapparent from the following detailed description of illustrativeembodiments that proceeds with reference to the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other aspects of the present invention are bestunderstood from the following detailed description when read inconnection with the accompanying drawings. For the purpose ofillustrating the invention, there are shown in the drawing exemplaryembodiments that are presently preferred, it being understood, however,that the invention is not limited to the specific instrumentalitiesdisclosed. Included in the drawings are the following figures:

FIG. 1 illustrates the decoding setting, according to some embodiments;

FIG. 2 illustrates how the imaging data for a plurality of subjects canbe processed into average per-subject low dimensional representations ofthe data;

FIG. 3A shows how multi-subject dimensionality reduction may be used toenhance the training and test process, according to some embodiments;

FIG. 3B shows how multi-subject denoising may be used to enhance thetraining and test process, according to some embodiments;

FIG. 4 illustrates an example framework for learning a generative modelof semantic representative in the brain, according to some embodiments.

FIG. 5 illustrates a fMRI-GAN coupled with a semantic decoder network,according to some embodiments;

FIG. 6 shows a framework for learning a decoder in an adversarialsetting, according to some embodiments;

FIG. 7 shows a module for assigning a semantic vector to words, phrasesor sentences used as stimuli in the system training data, according tosome embodiments;

FIG. 8 illustrates a generic decoding of semantic vector from functionalimages, according to some embodiments;

FIG. 9 provides a high-level overview of the mapping system, as it maybe implemented in some embodiments of the present invention.

FIG. 10 shows a recurrent neural network that can be used to implementthe mapping system illustrated in FIG. 9;

FIG. 11 provides an example of a parallel processing platform that maybe utilized to implement the machine learning models and other aspectsof the various workflows discussed herein.

DETAILED DESCRIPTION

The following disclosure describes the present invention according toseveral embodiments directed at methods, systems, and apparatusesrelated to improving decoding from brain imaging data of individualsubjects by using additional imaging data from other subjects. Thetechniques described herein are important for the purpose of improvingthe performance of brain decoding systems beyond what would be feasiblewith the functional MRI data from a single subject. These techniques canalso be used for denoising by re-representing the data from a subject toonly contain the information explained by latent variables. A secondimportant aspect is that it allows for data from multiple subjects to beused in building better models at one point in time (e.g., by an imagingcompany) and used much later to improve decoding on a new subject (e.g.,by an end user).

FIG. 1 illustrates the decoding setting, according to some embodiments.In this example, the subject has been presented the concept of a“table.” Using fMRI, a pattern of brain activation 105 is acquired. Thispattern of brain activation 105 is converted into a vector 110 with onevalue per voxel. The concept of “table” also has an associated semanticvector 115 in this example.

The patterns of activation for many concepts can be assembled into amatrix, with one pattern per row; a corresponding matrix can be createdfor the respective semantic vectors. In this setting, one may learn adecoding model M that predicts a set of target variables Y(characteristics) from fMRI data X_(train), so

Z _(train) =M(X _(train)).

Additionally, the values of target variables Y (characteristics) may bepredicted from imaging data X_(test), so

Z _(test) =M(X _(test)).

According to some embodiments, two different approaches are used forusing data from multiple subjects to improve decoding in test data froma single subject: dimensionality reduction and denoising. The techniquesdescribed herein utilize a group dimensionality reduction (GDR)technique (e.g., Shared Response Modelling, SRM, or generalizedCanonical Correlation Analysis, gCCA) which learns to decompose brainactivation in each subject as a combination of common, shared responses.In the GDR setting, the aim is to achieve functional alignment ofstimuli responses in distinct subjects assuming that the stimuli invokesimilar functional responses. Essentially, GDR maps the activationacross the subject's voxels to a new space that is shared between thesubjects.

FIG. 2 illustrates how the imaging data for a plurality of subjects canbe processed into average per-subject low dimensional representations ofthe data. In this example, a per-subject project matrix is applied tothe imaging data for each subject to yield the low dimensionalrepresentations of the subject's data. For example, in FIG. 2,projection matrix P1 is applied to the imaging data from subject 1 toyield low dimensional representation S1, P2 is applied to imaging datafrom subject 2 to yield low dimensional representation S2, etc. Then,the low dimensional representations from each subject are averaged toyield the average per-subject low dimensional representations for thepopulation (represented in FIG. 2 as S).

The example of FIG. 2 assumes that the response of each voxel to therange of stimuli is a combination of a small number of responsevariables, which represent characteristics of the stimuli. Additionally,this assumes that these response variables are present in all thesubjects (if they all respond in the same way) and that the activationthat is not being driven by the common response variables is irrelevant.The mapping can then be learned from these common variables, rather thanvoxels; it can then be applied to a similar transformation of new testdata, not used to fit the model, on which decoding is to be performed.

FIGS. 3A and 3B show two options for modifying the training and testprocedure with a single subject. FIG. 3A shows how multi-subjectdimensionality reduction may be used enhance the training and testprocess, according to some embodiments. Using a GDR technique, trainingdata from each subject is transformed into a low-dimensional space ofresponse variables shared by all subjects S_(train). The decoding modelis trained on these response variables S_(train) to produce Z_(train).This is illustrated in the top section of FIG. 3A. The transformationlearned there is applied to the test data of the individual subject, andthe decoding model applied to the resulting response variables. This isillustrated in the bottom of FIG. 3A.

FIG. 3B shows how multi-subject denoising may be used to enhance thetraining and test process, according to some embodiments. The trainingdata from each subject is transformed into a low-dimensional space ofresponse variables shared by all subjects S_(train) using GDR. Thetraining data is then transformed back into the original space, strippedof all activation that is not explained by the common response variables(denoted by X1 _(train), X2 _(train), and X3 _(train) in FIG. 3B). Thisis then used to learn the decoding model M, as illustrated in topportion of FIG. 3B. The same transformation to and from thelow-dimensional space is applied to the test data of the individualsubject, and the decoding model applied to this, as illustrated in thebottom of FIG. 3B.

The input to a GDR is a matrix X_(train) _(_) _(i) for each subject i,with #examples rows (time points, stimuli) and #voxels_i columns. GDRsallow the data of each subject to be transformed from #time points x#voxels to #time points x #response variables, where the latter isshared by all subjects. GDR may then be formulated as follows:

S _(i) =T _(i)(Xtrain_(i)),

where S_(i) is the representation of the subject i's stimuli imagingdata in the aligned functional space. T_(i) is the projection operatorthat performs the mapping from the voxel space to the shared voxelspace. For the purposes of generality, it may be assumed that thistransformation operation is subject-specific however it can alsoaccommodate a common projector. This transformation can be invertedthrough the use of an operator to yield a reconstruction transformationW_(i), i.e.

{circumflex over (X)} _(train) _(i) =W _(i) S _(i).

The techniques described herein rely on deriving a common representationS from all subject datasets X_(train) _(i) which correspond acrosssubjects who all saw the same stimuli, as

$S = {\sum\limits_{i = 1}^{m}S_{i}}$

from the representations S_(i)i of individual subjects. As describedearlier, the decoding setting is one where a machine learning model M islearned that predicts a set of target variables Z from imaging dataX_(train), thus

Z=M(X _(train))

and the values of target variables Y are predicted from imaging dataX_(test):

{circumflex over (Z)}=M(X _(test)).

The GDR can be learned from all datasets available for multiplesubjects, as described above, yielding a common representation S andtransformations T_(i)/W_(i) for each subject. The denoised dataset foreach subject is obtained by applying the reconstruction transformationto the common representation that yields {circumflex over (X)}_(train)_(i) . This is then used to learn the decoding model M in each personfrom a cleaned version of their data

Z=M({circumflex over (X)} _(train) _(i) ).

At test time, the dataset for each subject is projected to the commonspace and reconstructed using only the information that survives thatprojection, yielding

{circumflex over (Z)}=M(W _(i)(T _(i)(X _(test) _(i) ))).

The GDR can be learned from all datasets available for multiplesubjects, as described above, yielding a common representation S andtransformations T_(i)/W_(i) for each subject. In this case, theprediction model is learned from the common representation S, so

Z=M(S).

At test time, the dataset for each subject is projected to the commonspace, and the prediction generated using only the information thatsurvives that projection, yielding

{circumflex over (Z)}=M(T _(i)(X _(test) _(i) )).

In both approaches, it is also possible to collect the training data fora new subject after the GDR is learned, as long as the same stimuli areused. The transformations T_(i) and W_(i) can then be derived withrespect to the common representation S learned from all the existingsubjects.

The subject specific representations are usually obtained through anoptimization framework that combines problem elements that are deemedsignificant such as the combination of fidelity to the voxel data andshared response space. Perhaps one of the most straightforward ways offinding a shared response is to borrow elements from non-negative matrixfactorization literature. Although activation data is not constrained tobe positive, other forms of regularization can be used to enforcecommonality across distinct subjects. One representative technique fromthis class of method is the shared response model (SRM) that aims tofind a common response by finding orthogonal image spaces for eachsubject:

$\begin{matrix}{argmin} \\{W_{i}S}\end{matrix}{\sum\limits_{i = 1}^{N}{{X_{i} - {SW}_{i}}}}$s.t.  W_(i)W_(i)^(T) = I  

where S is the shared activation matrix and W_(i) encodes orthogonalimage spaces for each subject.

In SRM, the degree of freedom is given to each subject in selecting itsorthogonal image spaces. Given W_(i), it is then trivial to find therepresentation of the subject in the shared space:

S _(i) =X _(i) W _(i) ^(T),

where S_(i) can be used in subsequent learning tasks. A de-noisedrepresentation in the voxel space can be obtained as follows:

{circumflex over (X)} _(i) =S _(i) W _(i).

Because S is shared across all the subjects, it can be regarded as theactivation matrix of a super subject.

Other ways of using matrix factorization techniques can be devised toincorporate other forms of regularization such as box constraints on S.An alternative approach to finding representations in a shared spaceacross subjects can be achieved through by extracting highly correlatedimage spaces. Highly correlated image spaces between a pair of subjectscan imply functional alignment of the subjects. In statistics, canonicalcorrelation analysis (CCA) is used to find the projections of two setsof random variables that are maximally correlated: Given two sets ofrandom variables Y₁∈R^(N) and Y₂∈R^(M), the aim is to find z₁=Y₁w₁ ^(T)and Z₂=Y₂w₂ ^(T) such that the following is maximized:

$\rho = {\frac{z_{1}^{T}z_{2}}{{z_{1}}{z_{2}}}.}$

The solution to this problem is given by solving for the largesteigenvalue and the corresponding eigenvector of a generalized eigenvalueproblem utilizing self and cross covariance matrices of the two sets ofvariables. The subsequent pairs of a₁ and a₂ are found by usingeigenvalues of decreasing magnitudes. It is worth noting that thesubsequent canonical covariates are orthogonal within and across thedatasets.

CCA is extended to handle multiple sets of variables in a variety ofways optimizing for different criterion. These methods are collectivelycalled Generalized Canonicals Correlation Analysis (GCCA) and in ourpresentation we consider the variant that maximizes the sum ofcorrelations of every pair of datasets. GCCA finds canonical covariatesby solving a generalized eigenvalue problem derived from the self andcross covariance matrices. Borrowing from the SRM notation, we can thenwrite the following for each subject:

S _(i) =X _(i) W _(i) ^(T),

where W_(i) is the projection operator from the voxel space to thecommon response space. Unlike SRM, there is no orthogonality constrainton W_(i), however the resulting covariates encoded by S_(i) areorthogonal. We then define the super subject response as follows:

$S = {\sum\limits_{i = 1}^{m}{S_{i}.}}$

Given the individual shares responses and the super subject, we developtwo methods for subsequent learning tasks that leverage data from othersubjects. Our motivation stems from the fact that we might only be ableto isolate a subset of the activations in each subject reliably; howevercombined as a super subject, we are able to utilize information fromother subjects.

A separate issue with the GDR methods described above is that there isno guarantee that the response variables learned are particularlyinformative. They explain the brain activation common across subjects,regardless of whether it represents any of the features of interest orsomething else. In some embodiments, a variant of Shared ResponseModeling (referred to herein as supervised SRM or “SSRM”) may beapplied, which combines the process of learning an SRM with the processof learning a decoder of semantic features of the stimulus (a semanticvector Z as used herein). In doing so, it generates response variablesthat are particularly suitable for decoding, rather than just to explainall of the brain activation across subjects.

Supervised Shared Response Modeling

When data from multiple subjects are available under the sameexperimental stimuli, information across samples can be fused to obtaina more refined representation corresponding to the stimuli. This refinedrepresentation can be helpful in a discriminative setting such as forclassification or in a generative setting. Assume that we have Nsubjects where each subject's activity matrix is denoted by X, of sized_(i)×m where d_(i) is the number of voxels for subject i and m is thenumber of experimental concepts. The aim is to find a factorization ofX_(i) as follows:

X _(i) =W _(i) S

s·t·W _(i) ^(T) W _(i) =I.

In this factorization W_(i) is of size d×r and encodes the decompositionof each concept into r orthonormal components. S is of size r×d and itis shared across the subjects. S and the set of W_(i)'s, {W_(i)}, can befound by solving the following optimization problem:

${argmin}_{W_{i}S}{\sum\limits_{i = 1}^{N}{{X_{i} - {W_{i}S}}}_{F}^{2}}$s.t.  W_(i)^(T)W_(i) = I.

The optimization problem given above can be solved by alternatingminimization. The shared response can be updated using S=1/NΣ_(i=1)^(N)W_(i) ^(T)X_(i). The update step of {W_(i)} corresponds to computingthe polar decomposition of X_(i)S^(T) for each subject (i.e.,W_(i)=U_(i)V_(i) ^(T) where X_(i)S^(T)=U_(i)Σ_(i)V_(i) ^(T)).

Often the aim in extracting a shared response across subjects is tolearn classifiers or generative models corresponding to stimuli.However, these steps are usually independent (i.e., shared responsemodelling is succeeded by the learning process). Here, we aim to fusethe shared response modeling with the learning process. The jointapproach can enhance the overall performance as the shared responsemodeling is provided with labels that can aid in extracting relevantinformation from subjects. This approach is referred to herein asSupervised Shared Response Modeling (SSRM).

We briefly review the discriminative setting that we use together withthe shared response. Given a description of the experimental stimuli, Zof size m×f where m is the number of experimental stimuli as used aboveand f is the number of components used to express the stimuli, thefollowing model can be written as follows:

Z=S ^(T) B.

In this linear model, B encodes coefficients that map the sharedresponse to each component of the description of the stimuli. In someembodiments, because the stimuli is concerned with semanticrepresentation in the brain, a semantic representation may be used ofeach concept. Conventionally, given S, B can be learnt in a variety ofways that incorporate some form of regularization for B to avoid overfitting to the training data.

In SSRM shared response modeling and learning may be combined asfollows:

${{{argmin}_{{W_{i}S},B}\left( {1 - \alpha} \right)}{\sum\limits_{i = 1}^{N}{{X_{i} - {W_{i}S}}}_{F}^{2}}} + {\alpha {{Z - {S^{T}B}}}_{F}^{2}} + {{\alpha\beta}{B}_{F}^{2}}$s.t.  W_(i)^(T)W_(i) = I.

In SSRM, the relative weights of the response modeling part and learningpart are controlled with a parameter α∈[0,1] and B is regularized bypenalizing its norm that is controlled by the parameter B. SSRM isoptimized by using a two-step alternating procedure that updated S and({W_(i)},B) pair. Note that the update steps corresponding to the({W_(i)},B) pair de-couples naturally as they are not paired in a termin the SSRM formulation. S is then updated solving the following normalequations:

${\left( {{{N\left( {1 - \alpha} \right)}I} + {\alpha \; {BB}^{T}}} \right)S} = {{\left( {1 - \alpha} \right){\sum\limits_{i = 1}^{N}{W_{i}^{T}X_{i}}}} + {\alpha \; {{BZ}^{T}.}}}$

B is updated by solving the following normal equations:

(SS ^(T)+β1)B=SZ.

{W_(i)} is updated using the polar decomposition as mentioned above.

In discriminative learning settings it is customary to add a bias termto the coefficient matrix B to account for different offsets that canoccur in test and training datasets. The SSRM framework described hereincan include the bias term with a slight modification of the formulationas follows:

${{{{argmin}_{{W_{i}S},B,b_{0}}\left( {1 - \alpha} \right)}{\sum\limits_{i = 1}^{N}{{X_{i} - {W_{i}S}}}_{F}^{2}}} + {\alpha {{Z - {\left\lbrack {S^{T}1} \right\rbrack \left\lbrack {Bb}_{0} \right\rbrack}^{T}}}_{F}^{2}} + {{\alpha\beta}{B}_{F}^{2}{s.t.\mspace{11mu} W_{i}^{T}}W_{i}}} = {I.}$

In this formulation, b₀ is a column vector of bias terms that needs tobe learned together with B. The update steps given above are slightlymodified to incorporate b₀.

Generating Synthetic Brain Images for Training Brain Decoding Systems

In some embodiments, a generative adversarial framework is applied thatutilizes the semantic stimuli and their corresponding fMRI images tolearn to generate images from semantic stimuli. This can be consideredlearning to map the distribution of semantic representations to thespace of fMRI image distribution.

FIG. 4 illustrates an example fMRI Generative Adversarial Network (GAN)framework 400 for learning a generative model of semantic representativein the brain, according to some embodiments. As would be understood byone skilled in the art, a GAN comprises a generative model and adiscriminative model (typically implemented using neural networks) thatlearn to create synthetic data similar to known input data. In thisexample of FIG. 4, the generator 410 takes the semantic representationof the stimuli 405 as input and then generates an fMRI image 415. Thenthe discriminator 420 decides whether the generated image looksrealistic (i.e., shares similar characteristics with real fMRI images).The aim of the generator 410 is to be able to generate realisticrenderings of the brain that can pass the discriminator's 420 test andthe discriminator 420 tries to tell the generated images from the realacquisitions. This framework can be trained using techniques generallyknown in the art. Unlike conventional techniques, the generating processis driven through an implicit cost that stems from the discriminator420. The discriminator 420 can be optionally provided the correspondingstimuli vector from the semantic representation of the stimuli 405. Inthis case the discriminator tests if the provided pair is a valid pair.

The framework 400 shown in FIG. 4 confirms that the generated images aresimilar to real acquisitions; however the framework 400 does notguarantee that the generated images will be consistent with theparticular stimuli as the discriminator does not consider such acriterion. The optional semantic representation input to thediscriminator has the potential to learn this consistency given a largeamount of data but it can be limited when it is hard to obtain a largeamount of stimuli-fMRI acquisition pairs.

In some embodiments, to address the need to obtain a sufficient amountof stimuli-fMRI acquisition pairs, the framework 400 may be coupled witha semantic decoder network as illustrated in FIG. 5. The semanticdecoder network 505 takes the generated fMRI image 415 and generatesdecoded stimuli 510. The cost associated with the decoded stimuli 510helps driving the evolution of the generator together with thediscriminator 420. That is, generator 410 evolves with gradientsback-propagated from both the semantic decoder network 505 and thediscriminator 420. The semantic decoder network 505 can be pre-trainedor fully trained before integrating it with the framework 400. In thefirst case, the semantic decoder 505 can be trained within the framework400 whereas for the latter case, the semantic decoder network 505 can bekept fixed (i.e., not updated).

In other embodiments, a cyclic consistency constraint can be used toenforce to generate fMRI images that are in agreement with the stimuli.In this method, the GAN is used to generate text from a given fMRIimage. In principal this is similar to learning a semantic decoder butin an adversarial setting. This is illustrated in FIG. 6. Given an fMRIimage corresponding to stimuli 605, a generator 610 generates generatedstimuli 615. The discriminator 620 then produces a binary classification625 indicting whether or not the generated stimuli are meaningful. Theadversarial loss can be augmented with a handcrafted loss measuring thedistance of the generated and real stimuli 630.

In some embodiments, the networks described above can be connectedthrough a cyclic consistency constraint. The fMRI-GAN achieves themapping F(S)=I, where S is the input sematic vector and I is thegenerated input image. The adversarial decoder learns the mappingG(I)=S. The cyclic consistency is then the following constraints:G(F(S))≈S F(G(I))≈I. The first constraint encourages a semantic vectorto be mapped back to itself after going through F and G, respectively.The second constraint encourages an input image to be mapped back toitself after going through G and F, respectively. Unlike the firstapproach, the cyclic approach does not require labeled data (i.e.,stimuli-brain image pair but (weak) supervision can be integrated intothis framework as well).

The approaches described above for generating synthetic data can beextended to leverage data from multiple subjects. This can be achievedeither by extracting shared information using a preprocessing techniquesuch as canonical correlation analysis and its generalizations.Nonetheless, this can be as well achieved using a machine learningtechnique and can be further coupled with the frameworks describedabove.

Direct Mapping Between Brain Images and Stimulus Representations

State-of-the-art fMRI experiments often use complex stimuli, with theultimate goal being to identify what in the brain activation encodescharacteristics of those stimuli (e.g., visual, semantic, etc.). Theunderlying assumption is that semantic content can be represented as avector in a semantic space as shown in FIG. 7. More specifically, FIG. 7shows a module for assigning a semantic vector to words, phrases orsentences used as stimuli in the system training data, according to someembodiments. In this context, “decoding” means being able to infer whatthat semantic space representation would be for the semantic contentpresent in a particular brain image. This is often done by learning amapping that associates the presence of each characteristic with itseffect on the pattern of brain activation across voxels. This is thenused to decode those features from new brain imaging data as shown inFIG. 8.

Recent studies also reported reconstructions of the spatial structure ofnatural images, while simultaneously revealing their semantic content.The reconstruction of a natural image here was defined as the image thathad the highest posterior probability of having evoked the measuredresponse. To include the semantic information in the model, it was alsonecessary to annotate the semantic category of training set images byhuman observers.

In some embodiments of the present invention, a system is used fordecoding from multi-modality brain imaging data and directly mapping toany form of stimulus representations. The decoding system described hasseveral advantages compared to the current decoding techniques. First,it is unnecessary to quantify the content of the system input/output.Secondly, the system monitors the mental state of a patient under anycondition. Third, the system output is in a form that can be understoodby human (natural language, pictures, movies, sounds, etc.). Fourth, thesystem output can be adapted according to the working condition.

A very large neuroimaging dataset is a prerequisite for designing asystem that can directly map brain images to stimulus representations.This dataset should preferably include functional brain images from anymodality and corresponding stimuli that elicit the brain activation. Thestimuli can be any format of communication (e.g., reading texts,listening stories, watching movies) via different modalities of sense(e.g., visual, auditory, olfactory).

FIG. 9 provides a high-level overview of the mapping system, as it maybe implemented in some embodiments of the present invention. During thetraining phase the mapping system 905 is presented with a series ofbrain images (brain image #1, brain image #2, etc.) and the stimuli usedto generate the brain images. For example, the mapping system 905 ispresented with the text “the hospital wanted to hire a new doctor” andan fMRI image of the resulting brain activity (i.e., brain image #1).During the inference phase, new images are presented to the mappingsystem 905 and the system 905 outputs a picture output (e.g., exteriorof a hospital) or textual output (e.g., “he would be listed as criticaland be in an ICU.”).

Because it is impossible to acquire enough paired data and stimulus fromone subject, it is necessary to have a technique that is able tointegrate data acquired from multiple subjects and multiple sessions.The mapping system described herein uses GDR. In the GDR setting the aimis to achieve functional alignment of stimuli responses in distinctsubjects assuming that the stimuli invoke similar functional responses.In essence, GDR maps the activation across the subject's voxels to a newspace that is shared between the subjects. The other way of enrichingthe dataset is to utilize synthetic data as described in the previoussection.

Assuming we have already obtained enough paired data, the mapping modulecan be trained based on a Recurrent Neural Network such as a longshort-term memory (LSTM). One possible embodiment of the system showssubjects sentences while functional brain images are acquired, and thentrains the Recurrent Neural Network to produce the sequence of words ineach sentence given the corresponding brain image.

For training, the model receives input of size N derived from some textcorpus D in the form of pairs <s_i, v_i>, where v_i is a brainactivation pattern evoked by stimulus s_i. Note here s_i could be asegment of text, a short movie clip, a piece of music etc. Theparameters theta of the model are estimated so that given the vectorv_i, the reconstruction of the stimulus s_i is as accurate as possible,as measured with a cross-entropy criterion. During inference, the modelreceives a new brain activation pattern v_j and produces a certain typeof stimulus forming the prediction for the current brain image v_j. FIG.10 shows a recurrent neural network that can be used to implement themapping system illustrated in FIG. 9. In this example, the solid linerepresents the training procedure and the dashed line represents theinference procedure.

FIG. 11 provides an example of a parallel processing platform 1100 thatmay be utilized to implement the machine learning models and otheraspects of the various workflows discussed herein. This platform 1100may be used in embodiments of the present invention where NVIDIA CUDA™(or a similar parallel computing platform) is used. The architectureincludes a host computing unit (“host”) 1105 and a graphics processingunit (GPU) device (“device”) 1110 connected via a bus 1115 (e.g., a PCIebus). The host 1105 includes the central processing unit, or “CPU” (notshown in FIG. 11), and host memory 1125 accessible to the CPU. Thedevice 1110 includes the graphics processing unit (GPU) and itsassociated memory 1120, referred to herein as device memory. The devicememory 1120 may include various types of memory, each optimized fordifferent memory usages. For example, in some embodiments, the devicememory includes global memory, constant memory, and texture memory.

Parallel portions of a big data platform and/or big simulation platformmay be executed on the platform 1100 as “device kernels” or simply“kernels.” A kernel comprises parameterized code configured to perform aparticular function. The parallel computing platform is configured toexecute these kernels in an optimal manner across the platform 1100based on parameters, settings, and other selections provided by theuser. Additionally, in some embodiments, the parallel computing platformmay include additional functionality to allow for automatic processingof kernels in an optimal manner with minimal input provided by the user.

The processing required for each kernel is performed by a grid of threadblocks (described in greater detail below). Using concurrent kernelexecution, streams, and synchronization with lightweight events, theplatform 1100 of FIG. 11 (or similar architectures) may be used toparallelize portions of the model based operations performed in trainingor utilizing the smart editing processes discussed herein. For example,in embodiments where a convolutional neural network is used as themachine learning model, the platform 1100 can be used to performoperations such as forward and backward convolution, pooling,normalization, etc. Additionally, the parallel processing platform 1100may be used to execute multiple instances of a machine learning model inparallel. For example, multiple instances of the first machine modeldescribed above with respect to FIG. 1 may be executed in parallel withdifferent parameters to simultaneously generate the plurality of optionsthat the user is presented with (see step 120 in FIG. 1).

The device 1110 includes one or more thread blocks 1130 which representthe computation unit of the device 1110. The term thread block refers toa group of threads that can cooperate via shared memory and synchronizetheir execution to coordinate memory accesses. For example, in FIG. 11,threads 1140, 1145 and 1150 operate in thread block 1130 and accessshared memory 1135. Depending on the parallel computing platform used,thread blocks may be organized in a grid structure. A computation orseries of computations may then be mapped onto this grid. For example,in embodiments utilizing CUDA, computations may be mapped on one-, two-,or three-dimensional grids. Each grid contains multiple thread blocks,and each thread block contains multiple threads. For example, in FIG.11, the thread blocks 1130 are organized in a two dimensional gridstructure with m+1 rows and n+1 columns. Generally, threads in differentthread blocks of the same grid cannot communicate or synchronize witheach other. However, thread blocks in the same grid can run on the samemultiprocessor within the GPU at the same time. The number of threads ineach thread block may be limited by hardware or software constraints.

Continuing with reference to FIG. 11, registers 1155, 1160, and 1165represent the fast memory available to thread block 1130. Each registeris only accessible by a single thread. Thus, for example, register 1155may only be accessed by thread 1140. Conversely, shared memory isallocated per thread block, so all threads in the block have access tothe same shared memory. Thus, shared memory 1135 is designed to beaccessed, in parallel, by each thread 1140, 1145, and 1150 in threadblock 1130. Threads can access data in shared memory 1135 loaded fromdevice memory 1120 by other threads within the same thread block (e.g.,thread block 1130). The device memory 1120 is accessed by all blocks ofthe grid and may be implemented using, for example, DynamicRandom-Access Memory (DRAM).

Each thread can have one or more levels of memory access. For example,in the platform 1100 of FIG. 11, each thread may have three levels ofmemory access. First, each thread 1140, 1145, 1150, can read and writeto its corresponding registers 1155, 1160, and 1165. Registers providethe fastest memory access to threads because there are nosynchronization issues and the register is generally located close to amultiprocessor executing the thread. Second, each thread 1140, 1145,1150 in thread block 1130, may read and write data to the shared memory1135 corresponding to that block 1130. Generally, the time required fora thread to access shared memory exceeds that of register access due tothe need to synchronize access among all the threads in the threadblock. However, like the registers in the thread block, the sharedmemory is typically located close to the multiprocessor executing thethreads. The third level of memory access allows all threads on thedevice 1110 to read and/or write to the device memory. Device memoryrequires the longest time to access because access must be synchronizedacross the thread blocks operating on the device. Thus, in someembodiments, each fMRI dataset can be divided into segments using datalocality techniques generally known in the art. Then, each segment canbe processed in parallel using register memory, with shared and devicememory only being used as necessary to combine the results to providethe results for the complete dataset.

The embodiments of the present disclosure may be implemented with anycombination of hardware and software. For example, aside from parallelprocessing architecture presented in FIG. 11, standard computingplatforms (e.g., servers, desktop computer, etc.) may be speciallyconfigured to perform the techniques discussed herein. In addition, theembodiments of the present disclosure may be included in an article ofmanufacture (e.g., one or more computer program products) having, forexample, computer-readable, non-transitory media. The media may haveembodied therein computer readable program code for providing andfacilitating the mechanisms of the embodiments of the presentdisclosure. The article of manufacture can be included as part of acomputer system or sold separately.

While various aspects and embodiments have been disclosed herein, otheraspects and embodiments will be apparent to those skilled in the art.The various aspects and embodiments disclosed herein are for purposes ofillustration and are not intended to be limiting, with the true scopeand spirit being indicated by the following claims.

An executable application, as used herein, comprises code or machinereadable instructions for conditioning the processor to implementpredetermined functions, such as those of an operating system, a contextdata acquisition system or other information processing system, forexample, in response to user command or input. An executable procedureis a segment of code or machine readable instruction, sub-routine, orother distinct section of code or portion of an executable applicationfor performing one or more particular processes. These processes mayinclude receiving input data and/or parameters, performing operations onreceived input data and/or performing functions in response to receivedinput parameters, and providing resulting output data and/or parameters.

A graphical user interface (GUI), as used herein, comprises one or moredisplay images, generated by a display processor and enabling userinteraction with a processor or other device and associated dataacquisition and processing functions. The GUI also includes anexecutable procedure or executable application. The executable procedureor executable application conditions the display processor to generatesignals representing the GUI display images. These signals are suppliedto a display device which displays the image for viewing by the user.The processor, under control of an executable procedure or executableapplication, manipulates the GUI display images in response to signalsreceived from the input devices. In this way, the user may interact withthe display image using the input devices, enabling user interactionwith the processor or other device.

The functions and process steps herein may be performed automatically orwholly or partially in response to user command. An activity (includinga step) performed automatically is performed in response to one or moreexecutable instructions or device operation without user directinitiation of the activity.

The system and processes of the figures are not exclusive. Othersystems, processes and menus may be derived in accordance with theprinciples of the invention to accomplish the same objectives. Althoughthis invention has been described with reference to particularembodiments, it is to be understood that the embodiments and variationsshown and described herein are for illustration purposes only.Modifications to the current design may be implemented by those skilledin the art, without departing from the scope of the invention. Asdescribed herein, the various systems, subsystems, agents, managers andprocesses can be implemented using hardware components, softwarecomponents, and/or combinations thereof. No claim element herein is tobe construed under the provisions of 35 U.S.C. 112, sixth paragraph,unless the element is expressly recited using the phrase “means for.”

We claim:
 1. A computer-implemented method for decoding from brainimaging data of individual subjects by using additional imaging datafrom other subjects, the method comprising: receiving a plurality offunctional Magnetic Resonance Imaging (fMRI) datasets corresponding to aplurality of subjects, wherein (a) each fMRI dataset corresponds to adistinct subject and (b) each fMRI dataset comprises brain activationpatterns resulting from presentation of a plurality of stimuli to thedistinct subject; applying a group dimensionality reduction (GDR)technique to the example fMRI datasets to yield a low-dimensional spaceof response variables shared by the plurality of subjects; training amodel to predict a set of target variables based on the low-dimensionalspace of response variables shared by all subjects, wherein the set oftarget variables comprise one or more characteristics of the pluralityof stimuli.
 2. The method of claim 1, further comprising: receiving anew fMRI dataset corresponding to a new subject; applying the GDRtechnique to transform the new fMRI dataset into new response variablesin the low-dimensional space; and applying the model to the new responsevariables to predict one or more target variables.
 3. The method ofclaim 1, wherein the GDR technique is Shared Response Modelling.
 4. Themethod of claim 1, wherein the GDR technique is generalized CanonicalCorrelation Analysis.
 5. The method of claim 1, wherein the GDRtechnique is a supervised Shared Response Modelling technique thatcombines application of the GDR technique to the example fMRI datasetsand training of the model.
 6. The method of claim 1, wherein the one ormore characteristics comprise a visual representation of one or morestimulus included in the plurality of stimuli.
 7. The method of claim 1,wherein the one or more characteristics comprise a semanticrepresentation of one or more stimulus included in the plurality ofstimuli.
 8. The method of claim 1, wherein at least a portion of theplurality of fMRI datasets comprise synthetic datasets and the methodfurther comprises: generating the synthetic datasets using a GenerativeAdversarial Network (GAN) framework comprising a generator, adiscriminator, and a semantic decoder network, wherein the generatorevolves with gradients back-propagated from the semantic decoder networkand the discriminator.
 9. The method of claim 1, wherein at least aportion of the plurality of fMRI datasets comprise synthetic datasetsand the method further comprises: generating the synthetic datasetsusing a GAN framework comprising a generator and a discriminatorconnected using a cyclic consistency constraint that minimizes thedifference between the plurality of stimuli and generated stimuliproduced by the generator.
 10. The method of claim 1, wherein the modelcomprises a Recurrent Neural Network.
 11. A computer-implemented methodfor decoding from brain imaging data of individual subjects by usingadditional imaging data from other subjects, the method comprising:receiving a first set of functional Magnetic Resonance Imaging (fMRI)datasets corresponding to a plurality of subjects, wherein (a) each fMRIdataset corresponds to a distinct subject; (b) each fMRI datasetcomprises brain activation patterns resulting from presentation of aplurality of stimuli to the distinct subject, (c) each fMRI data is invoxel space; applying a group dimensionality reduction (GDR) techniqueto the first set of fMRI datasets to yield a low-dimensional space ofresponse variables shared by the plurality of subjects; generating asecond set of fMRI datasets corresponding to the plurality of subjectsby projecting the low-dimensional space of response variables back tovoxel space; training a model to predict a set of target variables basedon the second set of fMRI datasets, wherein the set of target variablescomprise one or more characteristics of the plurality of stimuli. 12.The method of claim 11, further comprising: receiving a first new fMRIdataset corresponding to a new subject in voxel space; applying the GDRtechnique to transform the new fMRI dataset into new response variablesin the low-dimensional space; generating a second new fMRI dataset byprojecting the low-dimensional space of response variables back to voxelspace; and applying the model to the second new fMRI dataset to predictone or more target variables.
 13. The method of claim 11, wherein theGDR technique is Shared Response Modelling.
 14. The method of claim 11,wherein the GDR technique is generalized Canonical Correlation Analysis.15. The method of claim 11, wherein the GDR technique is a supervisedShared Response Modelling technique that combines application of the GDRtechnique to the example fMRI datasets and training of the model. 16.The method of claim 11, wherein the one or more characteristics comprisea visual representation of one or more stimulus included in theplurality of stimuli.
 17. The method of claim 11, wherein the one ormore characteristics comprise a semantic representation of one or morestimulus included in the plurality of stimuli.
 18. The method of claim11, wherein at least a portion of the first set of fMRI datasetscomprise synthetic datasets and the method further comprises: generatingthe synthetic datasets using a Generative Adversarial Network (GAN)framework comprising a generator, a discriminator, and a semanticdecoder network, wherein the generator evolves with gradientsback-propagated from the semantic decoder network and the discriminator.19. The method of claim 11, wherein at least a portion of the first setof fMRI datasets comprise synthetic datasets and the method furthercomprises: generating the synthetic datasets using a GAN frameworkcomprising a generator and a discriminator connected using a cyclicconsistency constraint that minimizes the difference between theplurality of stimuli and generated stimuli produced by the generator.20. The method of claim 11, wherein the model comprises a RecurrentNeural Network.
 21. A system for decoding brain imaging data ofindividual subjects by using additional imaging data from othersubjects, the system comprising: a functional Magnetic Resonance Imaging(fMRI) scanner configured to acquire an fMRI dataset corresponding to asubject, wherein the fMRI dataset comprises brain activation patternsresulting from presentation of a plurality of stimuli to the distinctsubject; one or more processors configured to: apply a groupdimensionality reduction (GDR) technique to the fMRI dataset totransform it into a low-dimensional space of response variables sharedby a plurality of subjects, and applying a machine learning model to thetransformed fMRI dataset to predict one or more target variables.